A TORNADO warning was issued across New York City early Tuesday morning, urging locals to shelter in place.
Millions have also been warned about potential flash floods across the city.
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The tornado warning was issued to residents in Brooklyn and Queens. It expired just after 5am local time.
More than 80,000 people and 18 schools were potentially at risk.
Locals were urged to shelter in place in a basement or the lowest floor of their home.
New Yorkers were told to protect themselves from flying debris.
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More than seven million people are potentially at risk of flash flooding as the warning covers the boroughs of Staten Island, Brooklyn, Manhattan, Queens, and the Bronx.
Footage shared online showed the skyline lighting up as thunderstorms barreled through the city.
National Weather Service forecasters warned that between 1.5 and three inches of rain had already fallen and another three inches are possible.
Winds of 15mph had been swirling out of JFK and LaGuardia airports.
Footage showed motorists stranded as highways were flooded during the morning commute.
Dramatic video shared online showed cars struggling in the flash floods.
More than 1,000 schools and over 50 hospitals are potentially at risk.
The flash flood warning is in place until 7:30am EDT, according to the NWS.
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Forecasters warned overnight that thunderstorms have been moving across the state.
Heavy downpours to the north and west of New York City could produce floods.
Up to two inches of rain within the space of an hour hit parts of New Jersey on Monday night, according to NBC4.
More than 400,000 people are at risk in New Jersey as a flood warning remains in place until just after 6am local time.
The wet weather comes just weeks after Staten Island saw more than two inches of rain during the Labor Day weekend.
Locals were warned of high tides as Hurricane Earl intensified before later weakening.
Experts say the Atlantic hurricane season has had its quietest start for 30 years.
There have been only three named tropical storms so far this year – Alex in early June, and Bonnie and Colin at the start of July.
It is the first time since 1992 that no named storms have formed in the Atlantic Basin between July 3 and the end of August, said hurricane expert Phil Klotzbach.
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August became only the third time in 60 years without a named storm.
Dr. Klotzbach, a meteorologist at Colorado State University, said: "The long quiet stretch has been quite surprising given the robust La Nina in place in the tropical Pacific and warmer than normal tropical Atlantic sea surface temperatures."
